Files
galaxy/static/scripts/galaxy.base.js
T

709 lines
26 KiB
JavaScript

// requestAnimationFrame polyfill
(function() {
var lastTime = 0;
var vendors = ['ms', 'moz', 'webkit', 'o'];
for(var x = 0; x < vendors.length && !window.requestAnimationFrame; ++x) {
window.requestAnimationFrame = window[vendors[x]+'RequestAnimationFrame'];
window.cancelRequestAnimationFrame = window[vendors[x]+
'CancelRequestAnimationFrame'];
}
if (!window.requestAnimationFrame)
window.requestAnimationFrame = function(callback, element) {
var currTime = new Date().getTime();
var timeToCall = Math.max(0, 16 - (currTime - lastTime));
var id = window.setTimeout(function() { callback(currTime + timeToCall); },
timeToCall);
lastTime = currTime + timeToCall;
return id;
};
if (!window.cancelAnimationFrame)
window.cancelAnimationFrame = function(id) {
clearTimeout(id);
};
}());
// IE doesn't implement Array.indexOf
if (!Array.indexOf) {
Array.prototype.indexOf = function(obj) {
for (var i = 0, len = this.length; i < len; i++) {
if (this[i] == obj) {
return i;
}
}
return -1;
};
}
// Returns the number of keys (elements) in an array/dictionary.
function obj_length(obj) {
if (obj.length !== undefined) {
return obj.length;
}
var count = 0;
for (var element in obj) {
count++;
}
return count;
}
$.fn.makeAbsolute = function(rebase) {
return this.each(function() {
var el = $(this);
var pos = el.position();
el.css({
position: "absolute",
marginLeft: 0, marginTop: 0,
top: pos.top, left: pos.left,
right: $(window).width() - ( pos.left + el.width() )
});
if (rebase) {
el.remove().appendTo("body");
}
});
};
/**
* Sets up popupmenu rendering and binds options functions to the appropriate links
*/
function make_popupmenu(button_element, initial_options) {
/* Use the $.data feature to store options with the link element.
This allows options to be changed at a later time
*/
var element_menu_exists = (button_element.data("menu_options"));
button_element.data("menu_options", initial_options);
// If element already has menu, nothing else to do since HTML and actions are already set.
if (element_menu_exists) { return; }
button_element.bind("click.show_popup", function(e) {
// Close existing visible menus
$(".popmenu-wrapper").remove();
// Need setTimeouts so clicks don't interfere with each other
setTimeout( function() {
// Dynamically generate the wrapper holding all the selectable options of the menu.
var menu_element = $( "<ul class='dropdown-menu' id='" + button_element.attr('id') + "-menu'></ul>" );
var options = button_element.data("menu_options");
if (obj_length(options) <= 0) {
$("<li>No Options.</li>").appendTo(menu_element);
}
$.each( options, function( k, v ) {
if (v) {
menu_element.append( $("<li></li>").append( $("<a href='#'></a>").html(k).click(v) ) );
} else {
menu_element.append( $("<li></li>").addClass( "head" ).append( $("<a href='#'></a>").html(k) ) );
}
});
var wrapper = $( "<div class='popmenu-wrapper' style='position: absolute;left: 0; top: -1000;'></div>" )
.append( menu_element ).appendTo( "body" );
var x = e.pageX - wrapper.width() / 2 ;
x = Math.min( x, $(document).scrollLeft() + $(window).width() - $(wrapper).width() - 5 );
x = Math.max( x, $(document).scrollLeft() + 5 );
wrapper.css({
top: e.pageY,
left: x
});
}, 10);
setTimeout( function() {
// Bind click event to current window and all frames to remove any visible menus
// Bind to document object instead of window object for IE compat
var close_popup = function(el) {
$(el).bind("click.close_popup", function() {
$(".popmenu-wrapper").remove();
el.unbind("click.close_popup");
});
};
close_popup( $(window.document) ); // Current frame
close_popup( $(window.top.document) ); // Parent frame
for (var frame_id = window.top.frames.length; frame_id--;) { // Sibling frames
var frame = $(window.top.frames[frame_id].document);
close_popup(frame);
}
}, 50);
return false;
});
}
/**
* Convert two seperate (often adjacent) divs into galaxy popupmenu
* - div 1 contains a number of anchors which become the menu options
* - div 1 should have a 'popupmenu' attribute
* - this popupmenu attribute contains the id of div 2
* - div 2 becomes the 'face' of the popupmenu
*
* NOTE: make_popup_menus finds and operates on all divs with a popupmenu attr (no need to point it at something)
* but (since that selector searches the dom on the page), you can send a parent in
* NOTE: make_popup_menus, and make_popupmenu are horrible names
*/
function make_popup_menus( parent ) {
// find all popupmenu menu divs (divs that contains anchors to be converted to menu options)
// either in the parent or the document if no parent passed
parent = parent || document;
$( parent ).find( "div[popupmenu]" ).each( function() {
var options = {};
var menu = $(this);
// find each anchor in the menu, convert them into an options map: { a.text : click_function }
menu.find( "a" ).each( function() {
var link = $(this),
// why do we need the DOM (mixed with jq)?
link_dom = link.get(0),
confirmtext = link_dom.getAttribute( "confirm" ),
href = link_dom.getAttribute( "href" ),
target = link_dom.getAttribute( "target" );
// no href - no function (gen. a label)
if (!href) {
options[ link.text() ] = null;
} else {
options[ link.text() ] = function() {
// if theres confirm text, send the dialog
if ( !confirmtext || confirm( confirmtext ) ) {
var f;
// relocate the center panel
if ( target === "_parent" ) {
window.parent.location = href;
// relocate the entire window
} else if ( target === "_top" ) {
window.top.location = href;
//??...wot?
} else if ( target === "demo" ) {
// Http request target is a window named
// demolocal on the local box
if ( f === undefined || f.closed ) {
f = window.open( href,target );
f.creator = self;
}
// relocate this panel
} else {
window.location = href;
}
}
};
}
});
// locate the element with the id corresponding to the menu's popupmenu attr
var box = $( parent ).find( "#" + menu.attr( 'popupmenu' ) );
// For menus with clickable link text, make clicking on the link go through instead
// of activating the popup menu
box.find("a").bind("click", function(e) {
e.stopPropagation(); // Stop bubbling so clicking on the link goes through
return true;
});
// attach the click events and menu box building to the box element
make_popupmenu(box, options);
box.addClass("popup");
menu.remove();
});
}
// Alphanumeric/natural sort fn
function naturalSort(a, b) {
// setup temp-scope variables for comparison evauluation
var re = /(-?[0-9\.]+)/g,
x = a.toString().toLowerCase() || '',
y = b.toString().toLowerCase() || '',
nC = String.fromCharCode(0),
xN = x.replace( re, nC + '$1' + nC ).split(nC),
yN = y.replace( re, nC + '$1' + nC ).split(nC),
xD = (new Date(x)).getTime(),
yD = xD ? (new Date(y)).getTime() : null;
// natural sorting of dates
if ( yD ) {
if ( xD < yD ) { return -1; }
else if ( xD > yD ) { return 1; }
}
// natural sorting through split numeric strings and default strings
var oFxNcL, oFyNcL;
for ( var cLoc = 0, numS = Math.max(xN.length, yN.length); cLoc < numS; cLoc++ ) {
oFxNcL = parseFloat(xN[cLoc]) || xN[cLoc];
oFyNcL = parseFloat(yN[cLoc]) || yN[cLoc];
if (oFxNcL < oFyNcL) { return -1; }
else if (oFxNcL > oFyNcL) { return 1; }
}
return 0;
}
$.fn.refresh_select2 = function() {
var select_elt = $(this);
var options = { width: "resolve",
closeOnSelect: !select_elt.is("[MULTIPLE]")
};
return select_elt.select2( options );
}
// Replace select box with a text input box + autocomplete.
function replace_big_select_inputs(min_length, max_length, select_elts) {
// To do replace, the select2 plugin must be loaded.
if (!jQuery.fn.select2) {
return;
}
// Set default for min_length and max_length
if (min_length === undefined) {
min_length = 20;
}
if (max_length === undefined) {
max_length = 3000;
}
select_elts = select_elts || $('select');
select_elts.each( function() {
var select_elt = $(this);
// Make sure that options is within range.
var num_options = select_elt.find('option').length;
if ( (num_options < min_length) || (num_options > max_length) ) {
return;
}
if (select_elt.hasClass("no-autocomplete")) {
return;
}
/* Replaced jQuery.autocomplete with select2, notes:
* - multiple selects are supported
* - the original element is updated with the value, convert_to_values should not be needed
* - events are fired when updating the original element, so refresh_on_change should just work
*
* - should we still sort dbkey fields here?
*/
select_elt.refresh_select2();
});
}
/**
* Make an element with text editable: (a) when user clicks on text, a textbox/area
* is provided for editing; (b) when enter key pressed, element's text is set and on_finish
* is called.
*/
// TODO: use this function to implement async_save_text (implemented below).
$.fn.make_text_editable = function(config_dict) {
// Get config options.
var num_cols = ("num_cols" in config_dict ? config_dict.num_cols : 30),
num_rows = ("num_rows" in config_dict ? config_dict.num_rows : 4),
use_textarea = ("use_textarea" in config_dict ? config_dict.use_textarea : false),
on_finish = ("on_finish" in config_dict ? config_dict.on_finish : null),
help_text = ("help_text" in config_dict ? config_dict.help_text : null);
// Add element behavior.
var container = $(this);
container.addClass("editable-text").click(function(e) {
// If there's already an input element, editing is active, so do nothing.
if ($(this).children(":input").length > 0) {
return;
}
container.removeClass("editable-text");
// Handler for setting element text.
var set_text = function(new_text) {
container.find(":input").remove();
if (new_text !== "") {
container.text(new_text);
}
else {
// No text; need a line so that there is a click target.
container.html("<br>");
}
container.addClass("editable-text");
if (on_finish) {
on_finish(new_text);
}
};
// Create input element(s) for editing.
var cur_text = container.text(),
input_elt, button_elt;
if (use_textarea) {
input_elt = $("<textarea/>")
.attr({ rows: num_rows, cols: num_cols }).text($.trim(cur_text))
.keyup(function(e) {
if (e.keyCode === 27) {
// Escape key.
set_text(cur_text);
}
});
button_elt = $("<button/>").text("Done").click(function() {
set_text(input_elt.val());
// Return false so that click does not propogate to container.
return false;
});
}
else {
input_elt = $("<input type='text'/>").attr({ value: $.trim(cur_text), size: num_cols })
.blur(function() {
set_text(cur_text);
}).keyup(function(e) {
if (e.keyCode === 27) {
// Escape key.
$(this).trigger("blur");
} else if (e.keyCode === 13) {
// Enter key.
set_text($(this).val());
}
});
}
// Replace text with input object(s) and focus & select.
container.text("");
container.append(input_elt);
if (button_elt) {
container.append(button_elt);
}
input_elt.focus();
input_elt.select();
// Do not propogate to elements below b/c that blurs input and prevents it from being used.
e.stopPropagation();
});
// Add help text if there some.
if (help_text) {
container.attr("title", help_text).tooltip();
}
return container;
};
/**
* Edit and save text asynchronously.
*/
function async_save_text( click_to_edit_elt, text_elt_id, save_url,
text_parm_name, num_cols, use_textarea, num_rows, on_start, on_finish ) {
// Set defaults if necessary.
if (num_cols === undefined) {
num_cols = 30;
}
if (num_rows === undefined) {
num_rows = 4;
}
// Set up input element.
$("#" + click_to_edit_elt).live("click", function() {
// Check if this is already active
if ( $("#renaming-active").length > 0) {
return;
}
var text_elt = $("#" + text_elt_id),
old_text = text_elt.text(),
t;
if (use_textarea) {
t = $("<textarea></textarea>").attr({ rows: num_rows, cols: num_cols }).text( $.trim(old_text) );
} else {
t = $("<input type='text'></input>").attr({ value: $.trim(old_text), size: num_cols });
}
t.attr("id", "renaming-active");
t.blur( function() {
$(this).remove();
text_elt.show();
if (on_finish) {
on_finish(t);
}
});
t.keyup( function( e ) {
if ( e.keyCode === 27 ) {
// Escape key
$(this).trigger( "blur" );
} else if ( e.keyCode === 13 ) {
// Enter key submits
var ajax_data = {};
ajax_data[text_parm_name] = $(this).val();
$(this).trigger( "blur" );
$.ajax({
url: save_url,
data: ajax_data,
error: function() {
alert( "Text editing for elt " + text_elt_id + " failed" );
// TODO: call finish or no? For now, let's not because error occurred.
},
success: function(processed_text) {
// Set new text and call finish method.
if (processed_text !== "") {
text_elt.text(processed_text);
} else {
text_elt.html("<em>None</em>");
}
if (on_finish) {
on_finish(t);
}
}
});
}
});
if (on_start) {
on_start(t);
}
// Replace text with input object and focus & select.
text_elt.hide();
t.insertAfter(text_elt);
t.focus();
t.select();
return;
});
}
function init_history_items(historywrapper, noinit, nochanges) {
//NOTE: still needed for non-panel history views
var action = function() {
// Load saved state and show as necessary
try {
var stored = $.jStorage.get("history_expand_state");
if (stored) {
for (var id in stored) {
$("#" + id + " div.historyItemBody" ).show();
}
}
} catch(err) {
// Something was wrong with values in storage, so clear storage
$.jStorage.deleteKey("history_expand_state");
}
// If Mozilla, hide scrollbars in hidden items since they cause animation bugs
if ( $.browser.mozilla ) {
$( "div.historyItemBody" ).each( function() {
if ( !$(this).is(":visible") ) { $(this).find( "pre.peek" ).css( "overflow", "hidden" ); }
});
}
historywrapper.each( function() {
var id = this.id,
body = $(this).children( "div.historyItemBody" ),
peek = body.find( "pre.peek" );
$(this).find( ".historyItemTitleBar > .historyItemTitle" ).wrap( "<a href='javascript:void(0);'></a>" )
.click( function() {
var prefs;
if ( body.is(":visible") ) {
// Hiding stuff here
if ( $.browser.mozilla ) { peek.css( "overflow", "hidden" ); }
body.slideUp( "fast" );
if (!nochanges) { // Ignore embedded item actions
// Save setting
prefs = $.jStorage.get("history_expand_state");
if (prefs) {
delete prefs[id];
$.jStorage.set("history_expand_state", prefs);
}
}
} else {
// Showing stuff here
body.slideDown( "fast", function() {
if ( $.browser.mozilla ) { peek.css( "overflow", "auto" ); }
});
if (!nochanges) {
// Save setting
prefs = $.jStorage.get("history_expand_state");
if (!prefs) { prefs = {}; }
prefs[id] = true;
$.jStorage.set("history_expand_state", prefs);
}
}
return false;
});
});
// Generate 'collapse all' link
$("#top-links > a.toggle").click( function() {
var prefs = $.jStorage.get("history_expand_state");
if (!prefs) { prefs = {}; }
$( "div.historyItemBody:visible" ).each( function() {
if ( $.browser.mozilla ) {
$(this).find( "pre.peek" ).css( "overflow", "hidden" );
}
$(this).slideUp( "fast" );
if (prefs) {
delete prefs[$(this).parent().attr("id")];
}
});
$.jStorage.set("history_expand_state", prefs);
}).show();
};
action();
}
function commatize( number ) {
number += ''; // Convert to string
var rgx = /(\d+)(\d{3})/;
while (rgx.test(number)) {
number = number.replace(rgx, '$1' + ',' + '$2');
}
return number;
}
// Reset tool search to start state.
function reset_tool_search( initValue ) {
// Function may be called in top frame or in tool_menu_frame;
// in either case, get the tool menu frame.
var tool_menu_frame = $("#galaxy_tools").contents();
if (tool_menu_frame.length === 0) {
tool_menu_frame = $(document);
}
// Remove classes that indicate searching is active.
$(this).removeClass("search_active");
tool_menu_frame.find(".toolTitle").removeClass("search_match");
// Reset visibility of tools and labels.
tool_menu_frame.find(".toolSectionBody").hide();
tool_menu_frame.find(".toolTitle").show();
tool_menu_frame.find(".toolPanelLabel").show();
tool_menu_frame.find(".toolSectionWrapper").each( function() {
if ($(this).attr('id') !== 'recently_used_wrapper') {
// Default action.
$(this).show();
} else if ($(this).hasClass("user_pref_visible")) {
$(this).show();
}
});
tool_menu_frame.find("#search-no-results").hide();
// Reset search input.
tool_menu_frame.find("#search-spinner").hide();
if (initValue) {
var search_input = tool_menu_frame.find("#tool-search-query");
search_input.val("search tools");
}
}
// Create GalaxyAsync object.
var GalaxyAsync = function(log_action) {
this.url_dict = {};
this.log_action = (log_action === undefined ? false : log_action);
};
GalaxyAsync.prototype.set_func_url = function( func_name, url ) {
this.url_dict[func_name] = url;
};
// Set user preference asynchronously.
GalaxyAsync.prototype.set_user_pref = function( pref_name, pref_value ) {
// Get URL.
var url = this.url_dict[arguments.callee];
if (url === undefined) { return false; }
$.ajax({
url: url,
data: { "pref_name" : pref_name, "pref_value" : pref_value },
error: function() { return false; },
success: function() { return true; }
});
};
// Log user action asynchronously.
GalaxyAsync.prototype.log_user_action = function( action, context, params ) {
if (!this.log_action) { return; }
// Get URL.
var url = this.url_dict[arguments.callee];
if (url === undefined) { return false; }
$.ajax({
url: url,
data: { "action" : action, "context" : context, "params" : params },
error: function() { return false; },
success: function() { return true; }
});
};
$(document).ready( function() {
$("select[refresh_on_change='true']").change( function() {
var select_field = $(this),
select_val = select_field.val(),
refresh = false,
ref_on_change_vals = select_field.attr("refresh_on_change_values");
if (ref_on_change_vals) {
ref_on_change_vals = ref_on_change_vals.split(',');
var last_selected_value = select_field.attr("last_selected_value");
if ($.inArray(select_val, ref_on_change_vals) === -1 && $.inArray(last_selected_value, ref_on_change_vals) === -1) {
return;
}
}
$(window).trigger("refresh_on_change");
$(document).trigger("convert_to_values"); // Convert autocomplete text to values
select_field.get(0).form.submit();
});
// checkboxes refresh on change
$(":checkbox[refresh_on_change='true']").click( function() {
var select_field = $(this),
select_val = select_field.val(),
refresh = false,
ref_on_change_vals = select_field.attr("refresh_on_change_values");
if (ref_on_change_vals) {
ref_on_change_vals = ref_on_change_vals.split(',');
var last_selected_value = select_field.attr("last_selected_value");
if ($.inArray(select_val, ref_on_change_vals) === -1 && $.inArray(last_selected_value, ref_on_change_vals) === -1) {
return;
}
}
$(window).trigger("refresh_on_change");
select_field.get(0).form.submit();
});
// Links with confirmation
$( "a[confirm]" ).click( function() {
return confirm( $(this).attr("confirm") );
});
// Tooltips
// if ( $.fn.tipsy ) {
// // FIXME: tipsy gravity cannot be updated, so need classes that specify N/S gravity and
// // initialize each separately.
// $(".tooltip").tipsy( { gravity: 's' } );
// }
if ( $.fn.tooltip ) {
$(".tooltip").tooltip( { placement: 'top' } );
}
// Make popup menus.
make_popup_menus();
// Replace big selects.
replace_big_select_inputs(20, 1500);
// If galaxy_main frame does not exist and link targets galaxy_main,
// add use_panels=True and set target to self.
$("a").click( function() {
var anchor = $(this);
var galaxy_main_exists = (parent.frames && parent.frames.galaxy_main);
if ( ( anchor.attr( "target" ) == "galaxy_main" ) && ( !galaxy_main_exists ) ) {
var href = anchor.attr("href");
if (href.indexOf("?") == -1) {
href += "?";
}
else {
href += "&";
}
href += "use_panels=True";
anchor.attr("href", href);
anchor.attr("target", "_self");
}
return anchor;
});
});